Contacts of the helix formed by residues 450 - 467 (chain A) in PDB entry 1ORZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A GLY 3.8 22.0 - - - +
5A SER* 5.5 3.1 - - - -
6A VAL* 5.3 11.0 - - + +
191A ASN* 4.9 5.4 - - - +
447A LYS* 5.5 1.3 - - - -
448A PRO 3.7 7.0 - - - +
449A LEU* 1.3 93.2 - - - +
451A SER* 1.3 60.6 + - - +
452A ASP* 2.8 18.4 - - - +
453A LEU* 2.8 34.9 + - + +
454A GLY 3.1 8.0 + - - -
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Residues in contact with SER 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 5.9 1.2 - - - +
17A LYS 6.0 2.2 - - - -
18A TYR* 6.2 4.5 - - - -
19A HIS* 3.3 29.7 - - - -
20A ILE* 6.0 0.5 - - - +
209A ARG* 5.3 5.6 - - - +
449A LEU 3.9 0.6 + - - -
450A PRO* 1.3 73.3 - - - +
452A ASP* 1.3 52.1 + - - +
454A GLY* 3.2 2.8 + - - +
455A LYS* 2.6 48.5 + - - +
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Residues in contact with ASP 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A PRO* 2.8 25.1 - - - +
451A SER* 1.3 80.7 - - - +
453A LEU* 1.3 83.9 + - - +
455A LYS* 3.1 17.6 + - + +
456A GLU* 2.8 28.9 + - - +
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Residues in contact with LEU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A LEU* 2.7 13.8 - - + +
189A THR* 2.7 34.8 - - - +
190A HIS* 4.0 9.0 - - - +
191A ASN* 3.9 17.0 - - - +
448A PRO 4.6 0.4 - - - +
449A LEU* 3.0 25.4 - - + -
450A PRO* 2.8 23.5 + - + +
452A ASP* 1.3 100.8 + - - +
454A GLY* 1.3 59.8 + - - +
456A GLU* 2.8 29.6 - - + +
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Residues in contact with GLY 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE* 5.1 5.6 - - - -
188A LEU* 3.0 25.5 - - - +
198A ILE* 3.2 18.2 - - - +
209A ARG* 4.2 14.6 - - - -
450A PRO 3.1 8.4 + - - -
451A SER* 3.7 2.5 - - - -
453A LEU* 1.3 78.8 - - - +
455A LYS* 1.3 62.5 + - - +
457A SER 3.2 10.9 + - - -
458A ILE* 3.6 2.4 + - - +
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Residues in contact with LYS 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS* 4.4 16.6 - - + +
20A ILE* 5.6 0.4 - - + +
451A SER* 2.6 47.9 + - - +
452A ASP* 3.3 12.8 + - - +
454A GLY* 1.3 71.2 - - - +
456A GLU* 1.3 63.9 + - - +
458A ILE* 2.7 36.6 - - + +
459A ALA* 3.5 1.4 + - - +
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Residues in contact with GLU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ASP* 4.9 1.3 - - - +
187A LEU 4.0 13.9 - - - +
188A LEU* 4.7 0.7 - - + -
189A THR* 4.2 17.8 + - - +
245A ARG* 5.4 11.7 + - - +
246A ALA* 5.7 2.8 - - - -
452A ASP 2.8 13.7 + - - +
453A LEU* 2.8 25.0 + - + +
455A LYS* 1.3 76.2 - - - +
457A SER* 1.3 70.6 + - - +
459A ALA* 3.0 24.8 + - - +
460A ASN 4.6 0.3 + - - -
580A ASP* 5.0 7.6 - - - +
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Residues in contact with SER 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 4.5 3.3 - - - +
186A ASP* 2.9 28.4 - - - +
187A LEU 2.8 25.5 + - - -
188A LEU* 3.5 15.1 - - - +
198A ILE* 3.1 29.3 - - - +
245A ARG* 6.3 0.4 - - - +
454A GLY 3.2 1.0 + - - -
455A LYS 3.1 1.0 - - - -
456A GLU* 1.3 85.6 - - - +
458A ILE* 1.3 50.0 + - - +
460A ASN* 2.7 31.4 + - - -
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Residues in contact with ILE 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS* 6.0 4.5 - - + +
20A ILE* 5.8 5.8 - - + -
185A LEU* 4.8 4.7 - - - -
198A ILE* 4.2 2.4 - - + +
207A ILE* 3.9 31.6 - - + -
454A GLY 3.6 4.4 + - - +
455A LYS* 2.7 32.5 + - + +
457A SER* 1.3 79.0 - - - +
459A ALA* 1.3 57.0 + - - +
460A ASN* 4.2 0.7 - - - +
461A LEU* 2.7 36.8 + - + +
462A ASP* 3.0 42.2 + - - +
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Residues in contact with ALA 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ARG* 4.8 7.2 - - - +
455A LYS 4.6 1.8 - - - +
456A GLU* 3.0 18.1 + - - +
458A ILE* 1.3 85.2 - - + +
460A ASN* 1.3 64.4 + - - +
462A ASP* 3.2 5.6 + - - +
463A LYS* 3.0 25.0 + - - +
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Residues in contact with ASN 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 4.2 12.3 - - - +
186A ASP* 3.1 14.3 + - - +
245A ARG* 3.7 21.4 - - - +
457A SER 2.7 30.1 + - - -
458A ILE* 3.5 1.2 + - - +
459A ALA* 1.3 76.1 - - - +
461A LEU* 1.3 74.5 + - - +
463A LYS* 3.5 8.0 + - - +
464A LEU* 3.5 17.7 + - - +
531A LEU* 3.8 20.5 - - - +
534A GLN* 2.9 36.7 + - - +
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Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 4.1 11.4 - - + -
200A TYR* 4.4 18.6 - - + -
207A ILE* 4.1 26.0 - - + -
458A ILE* 2.7 25.1 + - + +
460A ASN* 1.3 81.1 - - - +
462A ASP* 1.3 66.6 + - - +
464A LEU* 3.2 7.5 + - + +
465A ARG* 3.2 48.9 + - - +
527A LEU* 3.8 13.7 - - + -
531A LEU* 3.7 25.6 - - + -
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Residues in contact with ASP 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A ILE* 3.0 46.8 + - - +
459A ALA* 3.2 7.6 + - - +
461A LEU* 1.3 82.3 - - - +
463A LYS* 1.3 64.1 + - - +
465A ARG* 3.1 13.5 + - - +
466A ASN* 3.0 33.8 + - - +
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Residues in contact with LYS 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A ALA 3.0 16.8 + - - +
460A ASN* 3.7 8.4 + - - +
462A ASP* 1.3 77.0 - - - +
464A LEU* 1.3 85.1 + - - +
466A ASN* 3.3 4.3 + - - +
467A ALA* 3.1 27.3 + - + +
511A PHE* 4.6 15.7 + - - -
512A ASP* 2.8 37.6 + - - +
514A VAL 4.1 12.0 + - - -
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Residues in contact with LEU 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A ASN 3.5 7.9 + - - +
461A LEU 3.2 9.3 + - - +
462A ASP 3.2 0.4 - - - -
463A LYS* 1.3 95.4 - - - +
465A ARG* 1.3 62.9 + - - +
467A ALA* 3.1 20.0 + - - +
511A PHE* 5.3 8.5 - - + -
514A VAL* 4.8 6.3 - - + +
515A LYS 4.5 3.8 - - - +
516A THR* 2.9 50.0 + - + +
527A LEU* 3.5 19.7 - - + -
530A THR* 2.8 32.8 - - - +
531A LEU* 3.1 20.6 - - + -
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Residues in contact with ARG 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A TYR* 4.1 14.3 + - - -
461A LEU* 3.2 34.7 + - - +
462A ASP* 3.1 17.6 + - - +
464A LEU* 1.3 82.4 - - - +
466A ASN* 1.3 65.7 + - - +
467A ALA 4.0 2.9 - - - +
468A ASN* 5.6 1.2 - - - +
516A THR* 4.6 5.3 + - - +
519A ARG* 3.1 82.9 + - + +
520A SER 5.4 0.4 + - - -
527A LEU* 3.1 35.0 - - - +
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Residues in contact with ASN 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A ASP* 3.0 24.0 + - - +
463A LYS* 4.0 4.2 - - - +
465A ARG* 1.3 82.6 - - - +
467A ALA* 1.3 64.4 + - - +
468A ASN* 3.4 7.3 + - - +
519A ARG* 4.7 8.6 + - - +
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Residues in contact with ALA 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A LYS* 3.1 24.6 + - + +
464A LEU 3.1 15.4 - - - +
465A ARG 4.0 2.1 - - - +
466A ASN* 1.3 76.7 - - - +
468A ASN* 1.4 57.4 + - - +
470A SER* 2.8 24.9 - - - +
512A ASP 5.6 0.7 - - - +
514A VAL 3.8 11.7 - - - +
515A LYS* 4.4 0.9 - - - -
516A THR 3.7 14.0 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il